At this point in time and space it is really impossible to figure out what will happen and when, I am sure that there will be expansions that will change a lot in how we build ships.
Flying cubes in space are fine, if I would engineer space ships probably they would all be cubes due to easy of docking and forming bigger structures, no wonder minecraft uses cubes to build stuff and imagine specific size cubes with life support just sticking to each other and forming a city. Also storing ships inside other ships is easier if they are same size and simple shape.
From PvP perspective most important thing to know is - will there be armor and how it will work, maybe 20 layers of armor would be better than shields, maybe we will have ships with huge "shields" in front to absorb damage, maybe we will have ships as small and as fast as possible so they are harder to hit.
But judging by how much money and time players are spending on cosmetics for their avatars I would say that majority of players will care what they are flying and how it looks like, but the beauty of Dual Universe is that we players will develop and change together with universe around us and our constructs will evolve over time, will be a lot of fun even if we end up flying giant cubes